matplotlib-users Mailing List for matplotlib

Hi,

I wrote a script to generate streamline plots using matplotlib a while 
ago, and this post inspired me to finally clean it up a bit. The code is 
available at http://web.mit.edu/speth/Public/streamlines.py and you can 
see an example of its output at 
http://web.mit.edu/speth/Public/streamlines.png

I'd be happy to have it find a home in matplotlib if it would be useful 
to other people there.

Ray

On 02/11/2011 11:10 AM, Gökhan Sever wrote:
> Hi,
> I see two related requests on:
> http://old.nabble.com/matplotlib-to-draw-streamlines--td28008708.html
> http://www.mail-archive.com/mat...@li.../msg07267.html
> a request filed on
> http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723
> <http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723>
> Is there any progress on this plot? Or source guides to implement such
> functionality in mpl?
> PS: The feature request @
> http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse
> <http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse> looks
> spammed? Anyone works on clearing these?
>
> --
> Gökhan
>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
>
>
>
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

On 2/11/11 9:45 AM, Jeff Whitaker wrote:
> On 2/11/11 9:10 AM, Gökhan Sever wrote:
>> Hi,
>> I see two related requests on:
>> http://old.nabble.com/matplotlib-to-draw-streamlines--td28008708.html
>> http://www.mail-archive.com/mat...@li.../msg07267.html
>> a request filed on
>> http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723
>> <http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723>
>> Is there any progress on this plot? Or source guides to implement such
>> functionality in mpl?
>> PS: The feature request @
>> http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse
>> <http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse>  looks
>> spammed? Anyone works on clearing these?
>>
>> -- 
>> Gökhan
> Gökhan:  Nobody is working on that as far as I know.  An interesting
> alternative to streamlines can be found here:
>
> http://scikits.appspot.com/vectorplot
>
> -Jeff
>
>
Gökhan:

I just added a lic_demo.py example to basemap SVN that shows how to use 
the vectorplot scikit with basemap (image as 
http://jswhit.fastmail.fm/lic_demo.png). Is this the sort of thing you 
were looking for?

-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

On Thu, Jan 20, 2011 at 4:44 AM, Stephan Markus <zw...@we...> wrote:
>
> Hello!
>
> I am also using two axes in a plot and want to be able to pick the lines of
> both axes.
> So far I used MPL 0.99.3 and a button on my interface to change the z-order
> of the axes in order to be able to pick lines of the "active" axes and to
> see the correct x/y data in the navigation toolbar. The callback code of my
> button is basically the code from othererik.
>
> Since MPL 1.0.0 I have the problem that lines of the second axes simply
> disappear from the plot whenever the plot is redrawn and it's zorder is
> higher.

This thread, in which I asked a similar question and receive a
workable solution from JJ, might be helpful.  I am now just
automatically moving all my lines over to the highest z-order axis so
that whatever is visible is pickable.  (But see below for a gotcha)

http://old.nabble.com/unable-to-point-pick-2nd-axis-after-upgrade-to-mpl-1.0-td30400311.html

On this note, to the developers:  This need to take into account the
z-order for picking lines has made my development more difficult.  I
have had a week's delay due to a difficult-to-understand bug in my
code in which I prematurely moved the line over to the highest z-order
axis, and then tried to format the axis with a custom
formatter--causing an error.  Simply moving the line only after all
formatting is done fixed the bug, but that wasn't obvious for a while.
The need to track which lines are on which z-order and to move them
only after all formatting/locating has been done on them strikes me as
a new "gotcha" that the simpler and more intuitive approach of "if you
can see it, you can pick it" didn't have. (I have a somewhat complex
case, though, in which there are three possible sorts of axes that
could wind up on either the right or left sides).

It also seems counter-intuitive that a line can "belong" to an axis
from the in Matplotlib and yet for the user it clearly is measured
using the other axis.  Could "z-order mattering" be toggled?  Anyway,
my 2 cents.

Thanks,
Che

On 2/11/11 9:10 AM, Gökhan Sever wrote:
> Hi,
> I see two related requests on:
> http://old.nabble.com/matplotlib-to-draw-streamlines--td28008708.html
> http://www.mail-archive.com/mat...@li.../msg07267.html
> a request filed on 
> http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723 
> <http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723>
> Is there any progress on this plot? Or source guides to implement such 
> functionality in mpl?
> PS: The feature request @ 
> http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse 
> <http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse> looks 
> spammed? Anyone works on clearing these?
>
> -- 
> Gökhan

Gökhan:  Nobody is working on that as far as I know.  An interesting 
alternative to streamlines can be found here:

http://scikits.appspot.com/vectorplot

-Jeff


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Hi,

I see two related requests on:

http://old.nabble.com/matplotlib-to-draw-streamlines--td28008708.html
http://www.mail-archive.com/mat...@li.../msg07267.html

a request filed on
http://sourceforge.net/tracker/index.php?func=detail&aid=3080981&group_id=80706&atid=560723

Is there any progress on this plot? Or source guides to implement such
functionality in mpl?

PS: The feature request @
http://sourceforge.net/tracker/?atid=560723&group_id=80706&func=browse looks
spammed? Anyone works on clearing these?

-- 
Gökhan

This is a slightly updated version of the script that uses subplots
instead of making you pop two windows, which doesn't seem to work like
I wanted it to on all systems.  None of the code that does the
locating has changed; only the demonstration part.

-- 
Daniel Hyams
dh...@gm...

Hi Ben,

On Thu, Feb 10, 2011 at 5:27 PM, Benjamin Root <ben...@ou...> wrote:
>
>
> On Thu, Feb 10, 2011 at 4:13 PM, Matthew Turk <mat...@gm...> wrote:
>>
>> Hi Ben,
>>
>> On Thu, Feb 10, 2011 at 5:06 PM, Benjamin Root <ben...@ou...> wrote:
>> > On Thu, Feb 10, 2011 at 1:38 PM, Matthew Turk <mat...@gm...>
>> > wrote:
>> >>
>> >> Hi there,
>> >>
>> >> I'm plotting some images in latitude/longitude space.  These are
>> >> images generated using the HEALpix method for discretizing the sphere,
>> >> but I have resampled them to a regular grid of phi, theta, and the
>> >> resultant image is contained in a variable img.  This is a fully-self
>> >> contained snippet:
>> >>
>> >> import matplotlib.figure
>> >> import matplotlib.backends.backend_agg
>> >> import numpy
>> >> from numpy import pi
>> >>
>> >> img = numpy.random.random((800, 800))
>> >> fig = matplotlib.figure.Figure((10, 4.9))
>> >> ax = fig.add_subplot(1,1,1,projection='mollweide')
>> >> image = ax.imshow(img, extent=(-pi,pi,-pi/2,pi/2), clip_on=False,
>> >> aspect=0.5)
>> >> cb = fig.colorbar(image, orientation='horizontal')
>> >> canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)
>> >> canvas.print_figure("hi.png")
>> >>
>> >> This makes a very nice looking figure, basically as expected: a black
>> >> oval outline for the map projection with the image inside it, the
>> >> lat/lon axes identified, etc.  What I'm running into here is that I
>> >> would like to fiddle with the size of the figure, to adjust the
>> >> whitespace and the position of the colorbar and so on, but any
>> >> adjustment to the height of the figure instantiation, for instance:
>> >>
>> >> fig = matplotlib.figure.Figure((10, 4.9))
>> >>
>> >> (and the rest unchanged) results in the black oval, the axes, but the
>> >> image content is completely blank.  Is this a bug, or just a subtlety
>> >> I'm missing?
>> >>
>> >> Thanks for any ideas!
>> >>
>> >> Best,
>> >>
>> >> Matt
>> >>
>> >
>> > I am curious, why are you saving the figure using canvas.print_figure()?
>> > How is it different from fig.savefig()?  If you, for some reason, must
>> > use
>> > canvas.print_figure(), then it seems like you are creating a new canvas
>> > from
>> > the figure  (I don't know, maybe it grabs figure's existing canvas
>> > object?).  In other words, you could just simply do:
>> >
>> > fig.savefig("hi.png")
>>
>> Maybe I'm doing something wrong here, but in the example script I gave
>> the figure does not have a canvas object affiliated with it; it's set
>> to None until I execute this operation:
>>
>> canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)
>>
>> At that point, fig.canvas is not None, and is the same canvas that I
>> just created:
>>
>> >>> print fig.canvas
>> None
>> >>> canvas = matplotlib.backends.backend_agg.FigureCanvasAgg(fig)
>> >>> canvas.print_figure("hi.png")
>> >>> fig.canvas
>> <matplotlib.backends.backend_agg.FigureCanvasAgg instance at 0x10263d3b0>
>> >>> canvas is fig.canvas
>> True
>>
>> >
>> > or, if you must use canvas.print_figure(), you could do:
>> >
>> > fig.canvas.print_figure()
>> >
>> > instead of the two lines you have right now.
>> >
>> > See if that makes a difference.
>>
>> Unfortunately it didn't end up making a difference.  The image is
>> still printed, with colorbar, with lat/lon lines, but no image in the
>> center of the black oval for the projection.
>>
>> Thanks,
>>
>> Matt
>>
>
> I just figured out why you don't have a canvas object.  It is because you
> aren't creating your figure object correctly.  Try this:
>
> import matplotlib.pyplot as plt
> import numpy
> from numpy import pi
>
> img = numpy.random.random((800, 800))
> fig = plt.figure(figsize=(10, 4.9))
> ax = fig.add_subplot(1,1,1,projection='mollweide')
> image = ax.imshow(img, extent=(-pi,pi,-pi/2,pi/2), clip_on=False,
> aspect=0.5)
> cb = fig.colorbar(image, orientation='horizontal')
> fig.savefig("hi.png")
>
> Notice that the figure is created through the pyplot's figure() method.
> Because pyplot knows the backend, it is able to assign the correct canvas
> object when making the figure object.  This can't be done from the Figure
> constructor alone.  Once a proper figure object is made, it can then
> properly call savefig().
>
> See if that helps!
> Ben Root
>
>

This script does work, but it gives exactly the same results as my
original script -- which is that if the figure size is set to (10,5.0)
it will include the image plot inside the black oval for the
projection, but if the figure size is (10,4.9) it will not.  I've
placed two images here:

http://imgur.com/CApcml&hc4ES
http://imgur.com/CApcm&hc4ESl

The first image was created with figsize (10,5).  The second was with
figsize (10,4.9).  The image plot does not appear in the second one,
although its bounding box does.  Any ideas?

Thanks!

Matt

  On 02/11/2011 03:48 AM, Jae-Joon Lee wrote:
> On Fri, Feb 11, 2011 at 8:38 AM, Jeff Layton<lay...@at...>  wrote:
>>   I hate to be the first one to comment on this post but I forgot to give
>> the error message and version of matplotlib. The error is,
>>
>> Traceback (most recent call last):
>>    File "./multi_file_test_2.py", line 460, in<module>
>>      ax.legend( (p1[0], p2[0]), ('IO Time', 'Total Elapsed Time'),
>> bbox_to_anchor=(1.05, 1), loc=2);
>>    File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
>> 3617, in legend
>>      self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
>> TypeError: __init__() got an unexpected keyword argument 'bbox_to_anchor'
>>
>>
>> The version of matplotlib I'm using is, 0.98.3-4ubuntu1
>>
>> Jeff
>>
> I'm quite sure that the *bbox_to_anchor* parameter is introduced later
> than 0.98.
> I think you have a few options,
>
>   * use "loc" parameter.
>   * see if "figlegend" helps.
>   * create a empty axes just for the purpose of drawing the legend.
>   * upgrade to 1.0.1 and I highly recommend it if you can.
>
> Regards,
>
> -JJ

I was worried about that. I will try to update my system but it's
an old Ubuntu 8.10 system. Looks like I have an excuse to
upgrade Ubuntu :)

Thanks!

Jeff

On Fri, Feb 11, 2011 at 8:38 AM, Jeff Layton <lay...@at...> wrote:
>  I hate to be the first one to comment on this post but I forgot to give
> the error message and version of matplotlib. The error is,
>
> Traceback (most recent call last):
>   File "./multi_file_test_2.py", line 460, in <module>
>     ax.legend( (p1[0], p2[0]), ('IO Time', 'Total Elapsed Time'),
> bbox_to_anchor=(1.05, 1), loc=2);
>   File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line
> 3617, in legend
>     self.legend_ = mlegend.Legend(self, handles, labels, **kwargs)
> TypeError: __init__() got an unexpected keyword argument 'bbox_to_anchor'
>
>
> The version of matplotlib I'm using is, 0.98.3-4ubuntu1
>
> Jeff
>

I'm quite sure that the *bbox_to_anchor* parameter is introduced later
than 0.98.
I think you have a few options,

 * use "loc" parameter.
 * see if "figlegend" helps.
 * create a empty axes just for the purpose of drawing the legend.
 * upgrade to 1.0.1 and I highly recommend it if you can.

Regards,

-JJ




>
>>    Good evening,
>>
>> I've been trying to find a way to move the legend outside
>> the plot so it doesn't cover it up. I've seen some things
>> online but I can quite get them to work (probably just my
>> lack of knowledge about matplotlib).
>>
>> The section of code creating the plot looks like,
>>
>>         fig = plt.figure()
>>         ax = fig.add_subplot(1,1,1);
>>
>>         p1 = ax.bar(ind, IO_Time_Plot, width, color="r", align='center');
>>         p2 = ax.bar(ind, Diff_Plot, width, color="y",
>> bottom=IO_Time_Plot, align='center');
>>
>>         ax.set_ylabel('Time (secs)');
>>         ax.set_title('Elapsed Time and IO Time',fontstyle='italic');
>>         ax.set_xticks(ind);
>>
>>         group_labels = [];
>>         for item in names:
>>            group_labels.append(item);
>>
>>         ax.set_xticklabels(group_labels);
>>
>>         fig.autofmt_xdate();
>>
>>         #ax.legend( bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.);
>>         ax.legend( (p1[0], p2[0]), ('IO Time', 'Total Elapsed Time'));
>>
>>
>>
>> You can see my attempt at moving the legend outside the bounding box
>> but when I try this, the legend never appears.
>>
>> TIA!
>>
>> Jeff
>>
>>
>>
>> ------------------------------------------------------------------------------
>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
>> Pinpoint memory and threading errors before they happen.
>> Find and fix more than 250 security defects in the development cycle.
>> Locate bottlenecks in serial and parallel code that limit performance.
>> http://p.sf.net/sfu/intel-dev2devfeb
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Matplotlib is great! I created all my figures in this paper [0] using matplotlib. I am impressed with the quality you get. I attach the plotting script for fig. 9, which does exactly what you want, I believe. There is a lot of other junk in there, so look for the "legend" function, it all happens in one line.

Cheers,
Paul.

[0] http://arxiv.org/abs/1011.3399, the paper should appear in phys. rev. B soon.

I've attached a small demo code that solves a problem I was having;
when the grid for the major and minor ticks are both drawn, the minor
grid is drawn over the top of the major grid.  This can make the grid
at the majors look a little messy.  The same thing was happening for
the ticks as well; minor ticks are drawn on top of major.

I'm hoping that someone will find the attached code useful, and also
that it might make its way into matplotlib.  The
"set_superior_locator" function in the attached code would be a very
natural fit inside the Locator class as a member function, with hardly
any modification.

All the set_superior_locator() function does is to inject itself into
the Locator object, so that it gets a chance to cull out locations
that are duplicated between it and its "superior" locator.  The main
use of this is to tell a minor locator who the major locator is, so
that the minor locator will not draw ticks and/or grid lines on top of
places where the major locator has already done it.

If you run the script attached, it will pop two plots (close one to
see the other); one with default drawing, and the second with the
culling of grid lines and tick marks.  I know that the colors and
thicknesses that I chose are ugly, but they do illustrate the point ;)

-- 
Daniel Hyams
dh...@gm...